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Transcriptome analysis and gene expression profiling of abortive and developing ovules during fruit development in hazelnut.

Cheng Y, Liu J, Zhang H, Wang J, Zhao Y, Geng W - PLoS ONE (2015)

Bottom Line: The results of the transcriptome assembly analysis revealed genetic information that was associated with the fruit development stage.These results were annotated using the public databases NR, NT, Swiss-Prot, KEGG, COG, and GO.A total of 1,637 and 715 unigenes were significantly upregulated and downregulated, respectively, in abortive ovules, compared with developing ovules.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Jilin Normal University, Siping, Jilin Province 136000, China.

ABSTRACT

Background: A high ratio of blank fruit in hazelnut (Corylus heterophylla Fisch) is a very common phenomenon that causes serious yield losses in northeast China. The development of blank fruit in the Corylus genus is known to be associated with embryo abortion. However, little is known about the molecular mechanisms responsible for embryo abortion during the nut development stage. Genomic information for C. heterophylla Fisch is not available; therefore, data related to transcriptome and gene expression profiling of developing and abortive ovules are needed.

Methodology/principal findings: In this study, de novo transcriptome sequencing and RNA-seq analysis were conducted using short-read sequencing technology (Illumina HiSeq 2000). The results of the transcriptome assembly analysis revealed genetic information that was associated with the fruit development stage. Two digital gene expression libraries were constructed, one for a full (normally developing) ovule and one for an empty (abortive) ovule. Transcriptome sequencing and assembly results revealed 55,353 unigenes, including 18,751 clusters and 36,602 singletons. These results were annotated using the public databases NR, NT, Swiss-Prot, KEGG, COG, and GO. Using digital gene expression profiling, gene expression differences in developing and abortive ovules were identified. A total of 1,637 and 715 unigenes were significantly upregulated and downregulated, respectively, in abortive ovules, compared with developing ovules. Quantitative real-time polymerase chain reaction analysis was used in order to verify the differential expression of some genes.

Conclusions/significance: The transcriptome and digital gene expression profiling data of normally developing and abortive ovules in hazelnut provide exhaustive information that will improve our understanding of the molecular mechanisms of abortive ovule formation in hazelnut.

No MeSH data available.


Species distribution of the BLASTX search results.This figure shows the species distribution of unigene BLASTX results against the NR protein database with a cutoff E-value < 10−5 and also shows the proportions of each species. Different colors represent different species. Species with proportions of less than 1% are not shown.
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pone.0122072.g002: Species distribution of the BLASTX search results.This figure shows the species distribution of unigene BLASTX results against the NR protein database with a cutoff E-value < 10−5 and also shows the proportions of each species. Different colors represent different species. Species with proportions of less than 1% are not shown.

Mentions: In order to annotate the unigenes, the unigene sequences were searched against the NR, NT, SwissProt, KEGG, COG, and GO databases with a cutoff E-value < 10−5. Annotation statistical data indicated that 37,080; 34,002; 23,585; 21,385; 13,345; and 28,642 unigenes were annotated, respectively. The 37,080 unigenes annotation results searched against the NR database are listed in S2 Table. In total, 38,810 unigenes returned a BLASTX result with a cutoff E-value < 10−5. The species distribution of the best match results were translated from BLASTX results as indicated in Fig 2. The C. heterophylla Fisch sequences showed the closest matches with Vitis vinifera (27.89%), followed by Prunus persica (26.78%), Ricinus communis (10.23%), Populus trichocarpa (9.76%), Fragaria vesca subsp. vesca (7.45%), and Glycine max (4.15%).


Transcriptome analysis and gene expression profiling of abortive and developing ovules during fruit development in hazelnut.

Cheng Y, Liu J, Zhang H, Wang J, Zhao Y, Geng W - PLoS ONE (2015)

Species distribution of the BLASTX search results.This figure shows the species distribution of unigene BLASTX results against the NR protein database with a cutoff E-value < 10−5 and also shows the proportions of each species. Different colors represent different species. Species with proportions of less than 1% are not shown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383543&req=5

pone.0122072.g002: Species distribution of the BLASTX search results.This figure shows the species distribution of unigene BLASTX results against the NR protein database with a cutoff E-value < 10−5 and also shows the proportions of each species. Different colors represent different species. Species with proportions of less than 1% are not shown.
Mentions: In order to annotate the unigenes, the unigene sequences were searched against the NR, NT, SwissProt, KEGG, COG, and GO databases with a cutoff E-value < 10−5. Annotation statistical data indicated that 37,080; 34,002; 23,585; 21,385; 13,345; and 28,642 unigenes were annotated, respectively. The 37,080 unigenes annotation results searched against the NR database are listed in S2 Table. In total, 38,810 unigenes returned a BLASTX result with a cutoff E-value < 10−5. The species distribution of the best match results were translated from BLASTX results as indicated in Fig 2. The C. heterophylla Fisch sequences showed the closest matches with Vitis vinifera (27.89%), followed by Prunus persica (26.78%), Ricinus communis (10.23%), Populus trichocarpa (9.76%), Fragaria vesca subsp. vesca (7.45%), and Glycine max (4.15%).

Bottom Line: The results of the transcriptome assembly analysis revealed genetic information that was associated with the fruit development stage.These results were annotated using the public databases NR, NT, Swiss-Prot, KEGG, COG, and GO.A total of 1,637 and 715 unigenes were significantly upregulated and downregulated, respectively, in abortive ovules, compared with developing ovules.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Jilin Normal University, Siping, Jilin Province 136000, China.

ABSTRACT

Background: A high ratio of blank fruit in hazelnut (Corylus heterophylla Fisch) is a very common phenomenon that causes serious yield losses in northeast China. The development of blank fruit in the Corylus genus is known to be associated with embryo abortion. However, little is known about the molecular mechanisms responsible for embryo abortion during the nut development stage. Genomic information for C. heterophylla Fisch is not available; therefore, data related to transcriptome and gene expression profiling of developing and abortive ovules are needed.

Methodology/principal findings: In this study, de novo transcriptome sequencing and RNA-seq analysis were conducted using short-read sequencing technology (Illumina HiSeq 2000). The results of the transcriptome assembly analysis revealed genetic information that was associated with the fruit development stage. Two digital gene expression libraries were constructed, one for a full (normally developing) ovule and one for an empty (abortive) ovule. Transcriptome sequencing and assembly results revealed 55,353 unigenes, including 18,751 clusters and 36,602 singletons. These results were annotated using the public databases NR, NT, Swiss-Prot, KEGG, COG, and GO. Using digital gene expression profiling, gene expression differences in developing and abortive ovules were identified. A total of 1,637 and 715 unigenes were significantly upregulated and downregulated, respectively, in abortive ovules, compared with developing ovules. Quantitative real-time polymerase chain reaction analysis was used in order to verify the differential expression of some genes.

Conclusions/significance: The transcriptome and digital gene expression profiling data of normally developing and abortive ovules in hazelnut provide exhaustive information that will improve our understanding of the molecular mechanisms of abortive ovule formation in hazelnut.

No MeSH data available.